Nothing
### Scorrect-model.tables.R ---
##----------------------------------------------------------------------
## Author: Brice Ozenne
## Created: Jan 12 2022 (09:41)
## Version:
## Last-Updated: Jan 12 2022 (11:45)
## By: Brice Ozenne
## Update #: 29
##----------------------------------------------------------------------
##
### Commentary:
##
### Change Log:
##----------------------------------------------------------------------
##
### Code:
## * Documentation
#' @title Estimate, Confidence Intervals, and P-value With Small Sample Correction
#' @description Extract estimate, standard error, confidence intervals and p-values associated to each coefficient of a latent variable model.
#' Similar to \code{lava::confint} but with small sample correction.
#' @name confint2
#'
#' @param object a \code{lvmfit} or \code{lvmfit2} object (i.e. output of \code{lava::estimate} or \code{lavaSearch2::estimate2}).
#' @param robust [logical] should robust standard errors be used instead of the model based standard errors? Should be \code{TRUE} if argument cluster is not \code{NULL}.
#' @param cluster [integer vector] the grouping variable relative to which the observations are iid.
#' @param as.lava [logical] when \code{TRUE} uses the same names as when using \code{stats::coef}.
#' @param transform [function] transformation to be applied.
#' @param conf.level [numeric, 0-1] level of the confidence intervals.
#' @param ssc [character] method used to correct the small sample bias of the variance coefficients: no correction (code{"none"}/\code{FALSE}/\code{NA}),
#' correct the first order bias in the residual variance (\code{"residual"}), or correct the first order bias in the estimated coefficients \code{"cox"}).
#' Only relevant when using a \code{lvmfit} object.
#' @param df [character] method used to estimate the degree of freedoms of the Wald statistic: Satterthwaite \code{"satterthwaite"}.
#' Otherwise (\code{"none"}/code{FALSE}/code{NA}) the degree of freedoms are set to \code{Inf}.
#' Only relevant when using a \code{lvmfit} object.
#' @param ... additional argument passed to \code{estimate2} when using a \code{lvmfit} object.
#'
#' @details When argument object is a \code{lvmfit} object, the method first calls \code{estimate2} and then extract the confidence intervals.
#'
#' @return A data.frame with a row per coefficient.
#'
#' @concept extractor
#' @keywords smallSampleCorrection
#' @export
`model.tables2` <- function(object, robust, cluster, transform,
as.lava, conf.level, ...) UseMethod("model.tables2")
## * model.tables.lvmfit
#' @export
model.tables.lvmfit <- function(x, ...){
x.confint <- confint(x, ...)
out <- cbind(summary(x, ...)$coef, upper = NA, lower = NA)
colnames(out)[1:4] <- c("estimate","se","statistic","p.value")
out <- out[,c("estimate","se","lower","upper","statistic","p.value")]
out[rownames(x.confint),"lower"] <- x.confint[,1]
out[rownames(x.confint),"upper"] <- x.confint[,2]
return(out)
}
## * model.tables2.lvmfit
#' @export
model.tables2.lvmfit <- function(object, robust = FALSE, cluster = NULL,
transform = NULL, as.lava = TRUE, conf.level = 0.95,
ssc = lava.options()$ssc, df = lava.options()$df, ...){
return(model.tables(estimate2(object, ssc = ssc, df = df, dVcov.robust = robust, ...),
robust = robust, cluster = cluster, as.lava = as.lava, conf.level = conf.level,
transform = transform))
}
## * model.tables.lvmfit2
#' @export
model.tables2.lvmfit2 <- function(object, robust = FALSE, cluster = NULL,
transform = NULL, as.lava = TRUE, conf.level = 0.95, ...){
dots <- list(...)
if(length(dots)>0){
warning("Argument(s) \'",paste(names(dots),collapse="\' \'"),"\' not used by ",match.call()[1],". \n")
}
## ** new model parameters
param <- coef(object, as.lava = as.lava)
name.param <- names(param)
n.param <- length(name.param)
## ** new Wald test
type <- object$sCorrect$skeleton$type
type <- type[!is.na(type$lava),]
null <- stats::setNames(rep(0, n.param),name.param)
if(any(type$detail %in% c("Sigma_var","Psi_var"))){
param.var <- type[type$detail %in% c("Sigma_var","Psi_var"),"param"]
if(as.lava){
null[names(object$sCorrect$skeleton$originalLink2param)[match(param.var,object$sCorrect$skeleton$originalLink2param)]] <- NA
}else{
null[object$sCorrect$skeleton$originalLink2param[match(param.var,object$sCorrect$skeleton$originalLink2param)]] <- NA
}
}
table.all <- compare2(object,
linfct = name.param,
rhs = null,
robust = robust,
cluster = NULL,
F.test = FALSE,
as.lava = FALSE,
sep = c("",""))
tableS.all <- summary(table.all, test = multcomp::adjusted("none"), transform = transform, conf.level = conf.level, rowname.rhs = FALSE)$table2
if(as.lava){
tableS.all <- tableS.all[names(object$sCorrect$skeleton$originalLink2param),,drop=FALSE]
}else{
tableS.all <- tableS.all[as.character(object$sCorrect$skeleton$originalLink2param),,drop=FALSE]
}
return(tableS.all)
}
## * model.tables.lvmfit2
#' @export
model.tables.lvmfit2 <- function(x, ...){ ## necessary as model.tables must have x has first argument
return(model.tables2(x, ...))
}
##----------------------------------------------------------------------
### Scorrect-model.tables.R ends here
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.